Sex: Male
Education:

• Doctor of Philosophy in Biology (Cell and Molecular Biology), University of the Philippines Diliman
• Bachelor of Science in Biology (Cell and Molecular Biology), University of the Philippines Los Baños

Field of Specialization:
Environmental Microbiology
Next Generation Sequencing
Genomics
Bioinformatics and Computational Biology
DNA Sequencing
DNA Extraction
Gel Electrophoresis

Researches:

Article title: Genetic diversity of penaeus monodon (Fabricius, 1798) in the Philippines as revealed by mitochondrial Cytochrome Oxidase I (COI)
Authors: Fredmoore L. Orosco and A.O. Lluisma
Publication title: Philippine Agricultural Scientist 101(1):84-92, March 2018

Abstract:
The mitochondrial cytochrome oxidase I (COI) marker, widely used in phylogenetic and DNA barcoding studies, may also be informative with respect to intraspecies diversity and regional scale population structure. It is particularly useful when data reported from other studies and relevant for comparative studies were mostly generated using this marker. In this study, the COI marker was used to investigate the genetic diversity and structure of populations of the black tiger shrimp, Penaeus monodon (Fabricius, 1798), in the Philippines. Wild specimens were obtained from six locations across the Philippine archipelago. Among the 146 COI sequences observed, only 15 haplotypes were identified of which only three were found to be frequent and widely distributed and the others were either unique to a site, or found in only two sites. The COI sequences therefore indicated that the six sites did not show significant genetic differentiation based on the Chi-square test, analysis of molecular variance (AMOVA), and FST analysis. However, comparison of the data with those reported for Thailand revealed that the Philippine populations have significantly lower haplotype and nucleotide diversity. The three widely distributed haplotypes in the Philippines were also observed in Thailand; these three haplotypes appeared to be the ancestral forms as suggested by the haplotype network analysis. The Philippine haplotypes showed less sequence divergence among themselves and clustered mostly in one major lineage of the tree, although two haplotypes were found to be highly divergent and clustered with other Thai haplotypes. The genetic diversity discovered in the study represents a significant resource; it also highlights opportunities for selection of better performing stocks.
Full text available upon request to the author

Article title: Prevalence, diversity, and co-occurrence of the white spot syndrome virus, monodon baculovirus and Penaeus stylirostris densovirus in wild populations of P. monodon in the Philippines
Authors: Fredmoore L. Orosco and Arturo O. Lluisma
Publication title: Diseases of Aquatic Organisms 125(3), August 2017

Abstract:
The farming of the black tiger shrimp Penaeus monodon in the Philippines relies on wild broodstock. PCR was thus used to determine the prevalence of white spot syndrome virus (WSSV), monodon baculovirus (MBV) and Penaeus stylirostris densovirus (PstDV) in a total of 178 shrimp from 6 geographically disparate locations where broodstock are captured for use in hatcheries. PCR amplicons were also sequenced to identify phylogenetic relationships of the virus haplotypes detected. Shrimp from southeastern Luzon (Camarines Norte) had the highest prevalence of each of the 3 viruses and were frequently co-infected with 2 or more viruses. No viruses were detected in shrimp from northwestern Luzon (Pangasinan). MBV was most prevalent and PstDV strains displayed the most genetic diversity. WSSV was detected at 3 sites, and a VP28 gene sequence examined was invariant and consistent with strains found in many countries, including Thailand, China, Japan, Korea, Indonesia, Iran, Brazil and Mexico. WSSV open reading frame 94 gene sequence analysis identified location-specific repeat types. MBV sequences were dissimilar to haplotypes detected in India. PstDV sequences were diverse and included 2 lineages detected either in Australia or in the United States, Ecuador, Taiwan, China and Vietnam. The PCR data confirmed that WSSV, MBV and PstDV are endemic in P. monodon in the Philippines but that populations at some locations might remain free of infection.
Full text link https://tinyurl.com/ebzve526

Article title: Variation in virome diversity in wild populations of Penaeus monodon (Fabricius 1798) with emphasis on pathogenic viruses
Authors: Fredmoore L. Orosco and Arturo O. Lluisma
Publication title: VirusDisease 28(3):1-10, July 2017

Abstract:
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing. Virome analysis of shrimp samples from different sites revealed distinct virome profiles, and hence significant differences in diversity, among the various sites based on number of OTUs, Shannon–Weaver Index, and Inverse Simpson Index. Sequences of key shrimp pathogens were detected such as the white spot syndrome virus (WSSV), and Penaeus stylirostris densovirus (PstDV). However, the patterns of distribution of the pathogenic viruses varied; whereas WSSV was found only in three out of six sites and PstDV was found in all but one site. The results also revealed shrimp-associated viruses that have not yet been observed in P. monodon such as avian virus-like, insect virus-like, plankton virus-like and bacteriophage-like sequences. Despite the diverse array of viruses detected in the study, a large proportion remains unidentified (i.e., similarity to sequences in the database was lower than the threshold required for definitive identification), and therefore could represent unexplored virus sequences and viral genomes in the environment.
Full text available upon request to the author

Article title: Genome Shuffling for Improved Thermotolerance, Ethanol Tolerance and Ethanol Production of Saccharomyces cerevisiae 2013
Authors: Fredmoore L. Orosco, Sean M. Estrada, Jessica F. Simbahan, Virgie A. Alcantara, Irene G. Pajares
Publication title: Decision Science Letters 10(01), January 2017

Abstract:
Bioethanol production has been the center of interest of scientists to generate a more sustainable, low cost and environment-friendly fuel compared to petroleum fuel products. However, a more robust and high performing ethanologen still needs to be developed to effectively convert sugars to ethanol while withstanding chemical and thermal stress. In this study, genome shuffling through ethyl methanesulfonate (EMS) mutagenesis and protoplast fusion was performed to develop superior strains of Saccharomyces cerevisiae 2013 with improved ethanol tolerance, thermotolerance and ethanol production. Results of the experiment obtained eight promising strains. These isolates exhibited higher ethanol yield compared to the parental strain at 30 o C and 42 o C. Furthermore, these isolates remained stable and viable up to 42 o C in 15 % (w v-1) to 18 % (w v-1) ethanol. Data on presence of trehalose content further supported these observations. Improved strain, F1D, was found to be the most promising isolate being able to grow at 42 °C and 18 % ethanol and yielding 10.83 % higher ethanol than parental strain 2013 and 15.16 % over the industrial strain S. cerevisiae HBY3. Thus, genome shuffling is a powerful tool in developing S. cerevisiae 2013 strains with improved fermentation qualities.
Full text link https://tinyurl.com/ydw3knm9

Article title: Genetic diversity of Kappaphycus species (Gigartinales, Rhodophyta) in the Philippines
Authors: Richard V. Dumilag, Fredmoore L. Orosco, Arturo O. Lluisma
Publication title: Systematics and Biodiversity 14(5):441-451, March 2016

Abstract:
The mariculture of eucheumatoids (species of Kappaphycus and Eucheuma) in the Philippines has had a long history, dating back to the 1970s. Over this period, a number of varieties have been brought into domestication; some are now widely distributed and farmed in various regions of the country, but a significant number appear to have a more restricted distribution and are farmed only in certain areas. The taxonomy of many of these seaweed cultivars and their phylogenetic relationships still remain to be resolved at the specific and subspecific levels. In this study, two mitochondrial DNA markers, COI-5P region and cox2-3 intergenic spacer, were used to assess the genetic diversity of the farmed varieties and a few specimens collected from the wild. Analysis using haplotype networks revealed several new haplotypes for K. alvarezii, K. malesianus and K. striatus, mainly from specimens collected from eastern and southwestern regions of the Philippines. The inferred phylogenetic relationships based on both mtDNA markers resolved the identity of all the materials used in the study at the species level. We present molecular evidence that K. malesianus, in addition to K. alvarezii, K. cottonii, K. inermis, K. procrusteanus and K. striatus (and, hence, all currently recognized species of Kappaphycus) occurs in the Philippines. Collectively, these observations suggest that the Philippine archipelago has richer genetic diversity of farmed and wild Kappaphycus than do the other geographic regions, consistent with the hypothesis that the Philippines is, or is part of, the centre of Kappaphycus biodiversity in the world. These findings also reveal an untapped diversity that can potentially be exploited for improving the commercial production of these carrageenophytes.
Full text available upon request to the author